chr1-150023307-G-A

Variant names:

• chr1-150023307-G-A
• rs67807996
• ENST00000764240.1:n.808-1948C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000764240.1(ENSG00000285184):​n.808-1948C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,042 control chromosomes in the GnomAD database, including 7,284 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (7284 hom., cov: 32)
• Consequence: ENSG00000285184 ENST00000764240.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 15 publications found

Genes affected

ENSG00000285184 (HGNC:58766):

OTUD7B (HGNC:16683): (OTU deubiquitinase 7B) Enables Lys48-specific deubiquitinase activity and thiol-dependent deubiquitinase. Involved in several processes, including negative regulation of I-kappaB kinase/NF-kappaB signaling; negative regulation of macromolecule metabolic process; and protein deubiquitination. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

LOC124904413 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000764240.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285184	ENST00000764240.1		n.808-1948C>T		intron	N/A
	ENSG00000285184	ENST00000764241.1		n.471-1948C>T		intron	N/A
	ENSG00000285184	ENST00000764242.1		n.376-1948C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42452 AN: 151924 Hom.: 7288 Cov.: 32

Gnomad AFR AF: 0.0777

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.323

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.279 AC: 42447 AN: 152042 Hom.: 7284 Cov.: 32 AF XY: 0.274 AC XY: 20331 AN XY: 74276

African (AFR) AF: 0.0776 AC: 3219 AN: 41490

American (AMR) AF: 0.279 AC: 4254 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1036 AN: 3468

East Asian (EAS) AF: 0.247 AC: 1276 AN: 5174

South Asian (SAS) AF: 0.310 AC: 1493 AN: 4820

European-Finnish (FIN) AF: 0.301 AC: 3165 AN: 10526

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.394 AC: 26802 AN: 67978

Other (OTH) AF: 0.321 AC: 677 AN: 2110

Alfa AF: 0.290 Hom.: 1074

Bravo AF: 0.272

Asia WGS AF: 0.223 AC: 775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.93
DANN	Benign	0.70
PhyloP100		-1.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs67807996; hg19: chr1-149995265;